MolNFT v1 · #97185 · protein
Atomic structure of bacteriophage HS1 tail needle knob
4K6B · HS1 knob domain: “Atomic structure of bacteriophage HS1 tail needle knob”. X-ray diffraction, 2 ligands (GLU, PO4), 5 pockets (best druggability 0.86). MolNFT v1 #97185 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4K6B
- Type
- protein
- Length
- 463 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HS1 knob domain
- Ligands
- GLU, PO4
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HS1 knob domain | protein | 154 | 13% helix, 45% strand | — |
| B | HS1 knob domain | protein | 156 | 13% helix, 44% strand | — |
| C | HS1 knob domain | protein | 153 | 12% helix, 45% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.86 | 0.96 | 30 | empty |
| 2 | 593 | 0.81 | 0.86 | 44 | empty |
| 3 | 98 | 0.62 | 0.88 | 21 | GLU |
| 4 | 92 | 0.61 | 0.88 | 22 | GLU |
| 5 | 86 | 0.61 | 0.89 | 20 | GLU |
Interfaces
3 interfaces between chains.
- A–B · 1200 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1199 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1191 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4K6B · Atomic structure of bacteriophage HS1 tail needle knob · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4K6B · PDBe 4K6B
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